Intrusion
by UnitedWhofans
Summary: What happens when a mysterious energy pulse is picked up by SHIELD and all that seems to be there is a Police telephone box?
1. Chapter 1

**AN: I do not own either Agents of S.H.I.E.L.D or Doctor Who. I'm bringing the two together for a little humor piece and not using them for profit. Spoilers for all of Doctor Who and for Agents up to 1x08**

**Intrusion**

"Where are Ward and May?"

Coulson was getting impatient. It was not like them to be late for an important meeting. He could see Fitzsimmons being late because of their work but they were here sitting next to Skye, who looked like a 5th grade student about to see a slide show in class; utterly bored.

Suddenly, Ward and May ran into the room, seemingly at the same time and they seemed very rushed.

"Where were you?"

"We were going over fighting techniques" they said in unison, as if they were practicing for what to say.

Coulson decided to ignore their odd behavior for the moment and focus on the task at hand. "At 0400 hours, our SHIELD satellites picked up an unusual energy pulse in the Andes Mountains. Further reconnaissance suggests that this pulse was attributed to a strange alien artifact….."

"Not another one! D'we need to prep for Ward going nuts again?" cracked Fitz, looking very pleased with himself. Simmons silenced him with an elbow nudge and turned to Coulson. "Do we know what it is, Sir?"

"We don't know what its function is. But we have pictures of it and going by our research, you two could be familiar with it" He then showed Fitzsimmons a picture.

"It's an old British police telephone box!" cried Simmons. She looked up again "In the Andes Mountains?" Coulson nodded.

"Mae mum gave me a little'un for good luck when we came here," Fitz recounted "It's in mae room. But to find such an old relic in a faraway place…"

"We will be there in an hour" Coulson went on. "Get your equipment ready. I have a feeling this will be something very interesting."

"By the way, what "mission level" is it?" asked Skye using air quotes, still very bored about what seemed to be just a simple mission.

"We don't know. We've never faced anything like this before and so we have no attachment to it" Coulson said and then left the room

"Figures" muttered Skye and the party dispersed to pack for this mysterious endeavor..

"I must say Clara, you have outdone yourself with this one. Those cookbooks in the library are doing you wonders."

The Doctor picked up a piece of roast beef with his fork and savored the taste as he bit into it. "I haven't had this good a meal since I dined with at the Savoy when Escoffier was there. Brilliant stuff." The Doctor gave a small golf clap.

Clara smiled and gave a fake bow and then she sat down to join him in the meal. She knew that the Doctor could very easily cook for them in the massive TARDIS kitchen. But to be honest, roasted tentacle of Rutan did not seem like an appetizing venture. So while she was doing this in order to save herself a lot of time in the marble bathroom, she was also looking for a hobby to carry on while aboard the TARDIS. A few days ago, she was picked up by the Doctor and was brought here. After questioning why, the Doctor explained that he was going to a secluded spot in order to conduct some experiments on alien forms of energy and he needed a person there to watch him and possibly take control of the TARDIS should he blow himself up or anything stupid like that.

"You know," said the Doctor, pulling Clara out of thought "I could take you to meet some great chefs if you are interested, And best of all, we can eat at their restaurants for free!" He pulled out his psychic paper and suddenly gave a stern look. "Food critic, London Times" he said and then grinned.

"We'd get soooooooo fat," said Clara, shaking her head

"I do have the gym and we spend a lot of energy in our line of work. Besides Time Lord metabolic rates are much different than you humans." The Doctor suddenly paused, a shade of fear crossing his face. "There was that one time though when I went on a diet…" He shivered "Carrot juice. Spawn of the devil."

"What?"

"Sorry. Got caught in a memory. Happens from time to time. Need not to worry. Well, back to work in the lab."

All the sudden, a klaxon went off. The Doctor stood up from the dining room table and went towards the rack of wines. He pulled a bottle, the wall rotated and the rack was replaced by a small monitor station. Clara was a bit shocked.

"Can never be too careful" explained the Doctor and he turned to the monitor. "It appears that we have some company. A craft has landed about 200 meters from our location. People are now coming out of the craft. It appears to be some sort of government organization and judging by the look of them, American."

"How do you know?"

"Who else but American government agents wear black suits and sunglasses in a place like this?"

"Oh, right."

The Doctor then began to speak softer , which was a signal to Clara that he was not addressing her.

"So it seems they are interested in you, old girl." He turned his attention back to Clara. "Well, nothing to worry about."

"How can you say that? Don't you keep a spare key in the phone compartment?"

"Ah, but the key only works for me and whoever I see fit. The entrance control to the TARDIS is purely isomorphic. The only way someone else gets in is if they somehow duplicate my fingerprints and hand structure and unless one of them is an extreme expert in biology and cellular formations, in addition to being knowledgeable of alien body makeup, then we have nothing to worry about. Let them look around." The Doctor finished his bold statements by putting his hands on his lapels, something Clara had seen to before to express stability and leadership.

_And total overconfidence_ she thought to herself.

"Oh look, we're getting audio" crowed the Doctor. "Let's see how they get on."

As the team approached the strange box, it was decided that Fitzsimmons should lead due to their knowledge concerning the look of the artifact. Fitz knew that the phone compartment would be a key point of interest. He opened it up and tried the phone.

"Nothing", he noted. But then his eye caught something. It was a small key. Fitz probably figured that the key went to the door, and so in an act of trying to prove himself, he went right to the door and began to try to open it.

Cries of "WHAT ARE YOU DOING" "YOU DON'T WHAT THAT COULD BE" and " FITZ, NO!" echoed in the mountain valley.

But to Fitz's disappointment and to everyone else's momentary relief, the door wouldn't open even though the key fit in the lock.

Fitz took the key back to the others and while Simmons was chastising him for attempting something very foolhardy, Coulson looked at the key and pondered.

"If it is alien, it would figure that this key could only be worked by the alien itself for protection. So in order to open the door, we need to simulate the alien's hand or capture the alien.

May looked on the ground near the doorway. "No footprints scorch marks or any sign of any being leaving the box. So we will have to assume that it's still inside."

"Wait a minute, have you guys lost your minds?" Ward cried "Look at how big it is. There's no way that anybody could be inside there with anything remotely dangerous. I don't think three of us could fit in there."

"Dangerous things come in all shapes and sizes of packages. The existence of Henry Pym should tell you that" warned Coulson, and then he turned his attention back to the key.

"They are very smart" admitted the Doctor. "But still unless one of them is an…..

Then the audio crackled to life. The man who appeared to be in charge called out "Simmons, you're our biology expert. Can you try and create a facsimile of this being's hand or what it uses to open this door?"

A brunette who looked like she was dressed up to either go to school or could have been a stereotypical exotic dancer in costume, but with those credentials the Doctor doubted it not that he was an expert on exotic dancing, came up to the man.

"Right away, Sir" She said "I'll start gathering biological information. I can see where I can find some already."

Clara turned to the Doctor, nervous but trying hard not to smile for seeing the Doctor caught up again in his own boisterousness. He seemed at a loss for words.

"Well, they...but I didn't…." and then Doctor uttered "Oh dear".

AN: Want me to continue? Please press the review button. Thank you for reading.


	2. Chapter 2

**AN: Thank you for the reviews and we shall continue. I do not own either AOS or Doctor Who. This chapter contains some cursing**

**Intrusion: Chapter 2**

Phil Coulson had seen a lot during his time with SHIELD.

He had met a billionaire who created a flying battle suit and who had fought alongside a Norse God, a WWII veteran who had been cryogenically preserved, and a doctor with a "very large" temper.

But even he was taken aback and lost for words when they opened up the mysterious blue box in the Andes.  
The others were more vocal in their surprise.

"HOLY SHIT!"

"NO FUCKING WAY!"

"BUT IT WAS JUST A SMALL BOX!"

"This is BRILLIANT!"

"Wonderful….."

Naturally the two young scientists were more apt to find the beauty in what they were currently viewing…

The Doctor gave a wide smile. "Always look forward to that reaction. That's why I was kind of taken aback at your reaction, Clara."

Clara tried to get the situation back on track. "Doctor, whatever the reaction is, they are inside the TARDIS and they seem to be getting a bit curious…."

"Oh, right. Well, let's think. We know they're smart; otherwise they wouldn't have gotten in. Now let's see how courageous these people are." He went to a side cupboard and pulled out a bit radio style microphone.

"Doctor, how can we possibly do that? We're outnumbered."

"Ever see _The Wizard of Oz?"_ he asked as he attached the microphone to an outlet.

Clara nodded and then the light bulb went off in her head…

While Ward, Skye and May were outside getting fresh air, the others were taking a closer look at

the inside of the "magic" box.

"Observations, please." ordered Coulson.

"The structure appears to be round. In the center is some sort of hexagonal console with an assortment of buttons and levers. In the center of this console is a column which leads up to what

appears to be a set of gigantic gears. The gears are rotating, in both directions alternatively" listed Fitz.

"In addition, there appear to be several entrances into this particular space. And surrounding the center console are railings which appear to have controls on them as well" added Simmons.

"Conclusion?" asked Coulson

"This "box" is some sort of laboratory or some kind of space craft" finished Fitzsimmons together.

"SPLENDID!" boomed a loud stern voice suddenly. "ALMOST IMPRESSIVE. NOW I WOULD ASK YOU TO KINDLY STEP OUT OF MY MACHINE. OTHERWISE, I WILL HAVE TO DEPLOY THE LASER GRID WHICH WILL VAPORIZE YOU ALL!"

"But Doctor, you don't have a laser grid on here"

"I know that. But they don't know that. And I know that they don't know that. And they know…

"Doctor…."

"Right. And now for the finishing touch…"

"What's going on?" said Ward, who had returned inside the box after getting his bearings back.

"Apparently, we're uninvited guests" explained Simmons. "We….."

She never got to finish her sentence as the lights suddenly shut off and a ghastly image began to

appear. It seemed to be the image of some sort of Egyptian god sitting on a throne. Then, the

eyes of this being turned green and then…

"KNEEL BEFORE THE MIGHT OF SUTEKH!"

"Good thing the TARDIS keeps an archival database of all the creatures I've seen. Now let's see." The Doctor turned back to the view screen. It appeared that the effect had worked in part, as he could see the small auburn haired man run right out of the TARDIS. Right behind him was the group's biological expert, if the Doctor remembered correctly. The other two men stayed very still and as the image dimmed and the lights went back on, the brown haired man, who the Doctor surmised was the leader of the group, said "That the best you've got? I've seen worse." The Doctor was intrigued by this man and noting the fact that nobody had touched anything since the group entered the TARDIS, decided to play the good cop. He spoke into the microphone in his normal tone.  
"Sorry about that. I do love a dramatic introduction from time to time. Well, I believe that you would want to meet with me. I'll tell you what. I'll give my location and a few directions and I will send a representative to meet you half way, if you follow my instructions. You go through the entrance on your left, go 3 doors down the corridor, take a left, pass by the swimming pool, take a right, pay the toll keeper to cross the bridge….

"What?" sasked Ward and Coulson at the same time.  
" Joking, there is no toll keeper. You cross the bridge and immediately make a left and I will be here in the dining room. Have fun. Oh and by the way, do not dare to touch anything. If you do, the laser grid will be used. Ta-ta."

The Doctor shook his head "Ta-ta? Never saying that again. Well Clara, I guess it's time to roll out the welcome wagon."

"Doctor, why do you want me to meet them halfway?"  
"A couple of reasons, my dear. One, I want to see if they can follow my directions and not get lost in the TARDIS. And two, you are much more of a people person than I am. You might soften their dispositions. Now hurry, I have to get the spare china ready."

AN: I know this probably wasn't as good as the last one but to be honest, the spark of the idea really only got me this far. If you have any ideas, let me know in the reviews. Thank you very much.


	3. Chapter 3

**AN: Thank you for liking and following this story. I hope that it continues to please you. Once again, I don't own either Doctor Who or Agents of S.H.I.E.L.D.**

**Intrusion Chapter 3**

"Are we there yet?" asked Fitz, "I'm starting to become doo-lally"

"We haven't even reached the bridge yet" asserted Coulson. "Keep moving".

It was decided that two of the team would stay at the entrance just in case this march inside the blue box turned out to be a ruse. May and Ward volunteered almost immediately, which was surprising to Coulson, but he accepted. Now he, Skye, and Fitzsimmons were trekking through this weird structure. While the corridors all looked the same and matched the traditional look of an outer space device or vehicle, the rooms were from all different styles of architecture. There was a swimming pool, a library, and what appeared to be some sort of enclave with ivy vines all over the walls. It was amazing to all of them, but especially to Fitzsimmons, who were calculating in their heads how this was all possible.

And whatever they had attempted to come up with was soon blown away when they finally came to the bridge.

It was the size of the George Washington Bridge. But it was in the style of the covered bridges of New England, except the walls were not made of wood; they were made of high strength glass, which was also the material for the floor. It was an awe inspiring sight. Below them was a river that flowed slowly. The river seemed to disappear into the horizons on each side. And that was another outstanding feature. The sky was still light but the sun was setting as if it were dusk.

"What is with this place?" questioned Skye "How far does it go? And why do I feel so relaxed?"

"I don't know but it is very fascinating." Simmons replied and she pulled out some sort of meter. "Ah. Apparently this ro…area is filled with positive ions. That explains the tranquility of it."

"Can we just rest here for a wee minute? I'm tuckered out" asked Fitz, who was bringing up the rear, "Besides how d'we know that this is the right way?" Before everybody turned to look at him like he was an idiot, he defended himself "I'mean, how d'we know there isn't more than one bridge in'ere?"

"We followed the voice's directions to the letter. I'm sure this is the right way." stated Coulson. "Come on, let's go."

"Och" grunted Fitz in frustration.

10 minutes later, they were still on the bridge, and even Coulson was beginning to doubt himself. Maybe the atmosphere of peace clouded his judgment. But then suddenly, he noticed something.  
"Get down!" he ordered and everybody obliged.

"Fitz, hand me the binoculars." He took them and put them to his eyes. He saw what appeared to be a girl sat down, leaning on the wall of the bridge. The girl was dark haired and appeared to be svelte in stature and body type. Surely this was not an enemy soldier. But he had seen stranger sights before.

He took down the binoculars and laid out his plan. "There appears to be somebody waiting for us up there. She doesn't look violent, but you can't be too careful. We'll move in as a team, but in case of trouble, I want you ready to move. Fitzsimmons, I want you guys to bail it back to the entrance. I've left infra-red markers indicating our path. Skye, you and me will have to try and stall this person or subdue her if things get out of hand. Are we clear?"

They all nodded. "Good, then we can proceed."

Skye and Coulson advanced as a pair with Fitzsimmons trailing for an easier escape route.

As they were nearing the creature, she seemed to sense their approach and turned towards them.

"Oh good, you made it. I was starting to wonder if he was going to leave me here on guard forever." She stood up and moved towards them. Skye and Coulson had their hands on their weapons. The tension mounted considerably, until for Skye it cracked.

As the girl reached out her hand, Skye pulled out her weapon, and in her best TV Cop voice, she yelled "HOLD IT RIGHT THERE, BITCH!" The girl was stunned and backed off.

Coulson shook his head is embarrassment. "Nice job, Kojak" he said sarcastically and pushed her arm down. He then turned to the girl, who also was now on edge. "You have to excuse her, she's relatively new to this line of work. My name is Phil Coulson, what's your name?" he asked in an attempt to defuse the situation.

The girl regained her composure. "Clara Oswald. I'm here to guide you the rest of the way."

"Nice to meet you. This is Skye and these two behind me are collectively known as Fitzsimmons." The scientists waved and immediately came up to talk, noticing Clara's English accent.

"Tis a verre interesting place." mused Fitz "But how…."

"Don't worry. The Doctor will tell you when we meet him. Speaking of which, we better get going."

As Clara led the procession further along the bridge, Simmons whispered to Fitz,

"What did she mean about a Doctor? Doctor who?"

AN: Please review and we'll see where it goes.


	4. Chapter 4

**AN: I see that this story is becoming very popular. I thank you for that. However, it is becoming a bit harder to determine where I want this story to go. So again, if you have any suggestions, please put them in your reviews. Once again, I do not own either property.**

**Intrusion Chapter 4**

Coulson was really starting to get annoyed, for several reasons.

His team was not at full capacity at the moment and despite it being the right move tactically, he was uncomfortable with the idea.

He was inside a blue box that seemed to have endless space on the inside and he was unable to understand the how and why of it.

He was being led to meet the owner of said box by a British girl who was not willing to answer any of his questions, only saying "Be patient. The Doctor will explain."

But most annoying of all, his two young scientists were like kids in a candy store and yakking up a storm about quantum mechanics and dimensions and other notions that he had no clue about.

_Is this routine procedure for them?_ he thought, _Lucky me._

He turned to Skye who just seemed in awe of the whole experience. She turned towards him and nodded, as if saying that she understood.

_Well, at least I'm not alone in my confusion._

Soon, the girl stopped in front of a large ornate door which clashed with the walls of the corridor.

"Here we are" she said and opened the door.

Inside was a massive dining room table which looked like it belonged in an old mansion. Above the table was a chandelier that completed the look of the room. Skye thought it looked so beautiful, like a fairy tale castle.

The next thing she spotted dimmed the mythos of the room, but added a bit more curiosity.

Standing at the end of the table looking into some sort of cabinet, was a man. From what Skye could tell, the man had a very, shall we say, unique taste in fashion. He was clad in a dark purple coat that went down to his thin legs. His shoes were black and very well tied. His hair was also fascinating; it was wavy, dark brown, and a bit long in the back, but not a mullet. He didn't seem to even notice that they had entered the room.

Suddenly, he twirled on a dime and faced them. Skye became even more intrigued. His face looked very alien yet there were human elements to it. He was wearing suspenders and a purple bow tie, which increased the uniqueness of his fashion sense, in Skye's eyes.

He gave a big grin and began to walk towards them.

"Ah, you made it! Well done, Clara and well done everyone. I'm glad that you didn't get lost. Last one took 2 days to find. Turned out he was in the television room. Said he found the old girl unlocked. Never did that again. But I ramble, Hello!" he finally reached them and held out his hand. "I'm the Doctor. And you are…"

Before Coulson could get a word out, the two Brits pushed through and eagerly presented themselves to the Doctor. They seemed to be like schoolchildren in front of their hero.

"H-H-Hi, Jemma Simmons, biochemist. This is Leo Fitz, engineer." Fitz let out a small, meekish "Hello". Simmons continued on, "But you can call us Fitzsimmons as a pair."

The Doctor looked puzzled but slowly began to get it. He began to chuckle and laugh and not sarcastically. "Oh that's a good one. Fitzsimmons. It's perfect, isn't it Clara?" He turned to Clara who gave him a bit of an eye. Instantly, the Doctor calmed down and proceeded. "Ahem. Right. So you are the one who was able to open the door. Very clever, Miss Simmons, you are very bright.

Simmons beamed with pride.

The Doctor then turned towards Skye. "And you are….."

"Skye. Computer specialist," she said in a low key manner and shook the Doctor's hand.

"You're the one who tried to pull that cop routine. Very tenacious and headstrong. Just like Zoe."

"What? How…"

'I saw the whole thing on my monitor. As for Zoe, never mind. A person that I knew a long time ago; A phantom memory from the past." He looked forlorn for a second but quickly shook it off.

He turned to face Coulson.

"Agent Phil Coulson."

"Ah, the leader of this merry bunch. Fearless and determined. A pleasure to meet you. Now, that introductions are out of the way, we can get on with further…Wait, I forgot to ask about the other two near the entrance."

"Ward and May. Physical trainers and experts in combat" said Simmons.

"Thank you my dear, I might as well take a look in on them to see that they haven't touched anything." He ran back to the monitor and switched the feed to the main control room. He jumped back as if he was shocked by something.

"Ummm..Mr. Coulson? Does your government usually approve of inter-squad relations?"

"What are you talking about?" demanded Coulson.

"Ah yes. Well, em….it seems that Mr. Ward and Miss May are being very friendly towards each other"

Everybody hurried to the monitor. Fitzsimmons, Skye, and Coulson were dumbfounded. There were Ward and May leaning on the door of the TARDIS, locked in full make out mode.

"I do hope they don't progress past this stage. I just got the TARDIS floor cleaned from the Yeti incident a few weeks back."

**AN: Please review and thanks once again. **


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